Categorial Grammar

The paper is a review article comparing a number of approaches to natural language syntax and semantics that have been developed using categorial frameworks. It distinguishes two related but distinct varieties of categorial theory, one related to Natural Deduction systems and the axiomatic calculi of Lambek, and another which involves more specialized combinatory operations

High Performance Computing of Gene Regulatory Networks using a Message-Passing Model

Gene regulatory network reconstruction is a fundamental problem in computational biology. We recently developed an algorithm, called PANDA (Passing Attributes Between Networks for Data Assimilation), that integrates multiple sources of 'omics data and estimates regulatory network models. This approach was initially implemented in the C++ programming language and has since been applied to a number of biological systems. In our current research we are beginning to expand the algorithm to incorporate larger and most diverse data-sets, to reconstruct networks that contain increasing numbers of elements, and to build not only single network models, but sets of networks. In order to accomplish these "Big Data" applications, it has become critical that we increase the computational efficiency of the PANDA implementation. In this paper we show how to recast PANDA's similarity equations as matrix operations. This allows us to implement a highly readable version of the algorithm using the MATLAB/Octave programming language. We find that the resulting M-code much shorter (103 compared to 1128 lines) and more easily modifiable for potential future applications. The new implementation also runs significantly faster, with increasing efficiency as the network models increase in size. Tests comparing the C-code and M-code versions of PANDA demonstrate that this speed-up is on the order of 20-80 times faster for networks of similar dimensions to those we find in current biological applications

Synchronising C/C++ and POWER

Shared memory concurrency relies on synchronisation primitives: compare-and-swap, load-reserve/store-conditional (aka LL/SC), language-level mutexes, and so on. In a sequentially consistent setting, or even in the TSO setting of x86 and Sparc, these have well-understood semantics. But in the very relaxed settings of IBM®, POWER®, ARM, or C/C++, it remains surprisingly unclear exactly what the programmer can depend on. This paper studies relaxed-memory synchronisation. On the hardware side, we give a clear semantic characterisation of the load-reserve/store-conditional primitives as provided by POWER multiprocessors, for the first time since they were introduced 20 years ago; we cover their interaction with relaxed loads, stores, barriers, and dependencies. Our model, while not officially sanctioned by the vendor, is validated by extensive testing, comparing actual implementation behaviour against an oracle generated from the model, and by detailed discussion with IBM staff. We believe the ARM semantics to be similar. On the software side, we prove sound a proposed compilation scheme of the C/C++ synchronisation constructs to POWER, including C/C++ spinlock mutexes, fences, and read-modify-write operations, together with the simpler atomic operations for which soundness is already known from our previous work; this is a first step in verifying concurrent algorithms that use load-reserve/store-conditional with respect to a realistic semantics. We also build confidence in the C/C++ model in its own terms, fixing some omissions and contributing to the C standards committee adoption of the C++11 concurrency model

Levenshtein distances fail to identify language relationships accurately

The Levenshtein distance is a simple distance metric derived from the number of edit operations needed to transform one string into another. This metric has received recent attention as a means of automatically classifying languages into genealogical subgroups. In this article I test the performance of the Levenshtein distance for classifying languages by subsampling three language subsets from a large database of Austronesian languages. Comparing the classification proposed by the Levenshtein distance to that of the comparative method shows that the Levenshtein classification is correct only 40% of the time. Standardizing the orthography increases the performance, but only to a maximum of 65% accuracy within language subgroups. The accuracy of the Levenshtein classification decreases rapidly with phylogenetic distance, failing to discriminate homology and chance similarity across distantly related languages. This poor performance suggests the need for more linguistically nuanced methods for automated language classification tasks